rdkit-chem gem

GEM for RDKIT, an Open-Source Cheminformatics Software

• cmake 3.8 or later
• curl
• tar, sed, make (those should be present anyway)
• SWIG 2 or later
• python header (python-dev)
• sqlite (sqlite3-dev)
• boost > 1.58 (libboost-all-dev)
• gcc

gem install rdkit_chem

It downloads the sources, compiles and installs RDKIT with the ruby bindings. The installation may last very long - please be patient.

Error:

CMake Error: Found package configuration file boost_serialization-config.cmake
but it set boost_serialization_FOUND to FALSE
Reason: No suitable build variant has been found.

Solution: The gem has been updated to use static Boost flags (-DBoost_USE_STATIC_LIBS=ON -DBoost_USE_STATIC_RUNTIME=ON).

Error:

Undefined symbols for architecture x86_64:
  "_rb_define_class", "_rb_str_new", ... (Ruby C API symbols)

Solution: Fixed in Code/RubyWrappers/gmwrapper/CMakeLists.txt with -undefined dynamic_lookup for macOS.

Error:

require 'RDKitChem'
# => TypeError: wrong argument type nil (expected Data)

Cause: Ruby 3.2+ introduced a new Data class that conflicts with SWIG's wrapper generation.

Workaround: Use Ruby 3.1.x:

# Using asdf
asdf install ruby 3.1.6
asdf set ruby 3.1.6

# Using rbenv
rbenv install 3.1.6
rbenv local 3.1.6

Error:

error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
error: no member named 'finite' in namespace 'std::__math'

Cause: CMake finds Xcode SDK Ruby headers instead of ruby/setup-ruby installed headers.

Solution: Fixed in extconf.rb by explicitly passing Ruby paths to CMake.

Full Clean Build:

rm -rf rdkit/build rdkit_chem
ruby ext/rdkit_chem/extconf.rb

Resume Interrupted Build:

cd rdkit/build
make -j8
make install

Test Loading:

DYLD_LIBRARY_PATH=$PWD/rdkit_chem/lib ruby -I $PWD/rdkit_chem/lib -e 'require "RDKitChem"; puts "Success!"'

• Full build takes ~20 minutes
• Some BOOST_NO_CXX98_FUNCTION_BASE warnings during build are harmless
• For detailed troubleshooting, see MACOS_BUILD_NOTES.md